When comparing DNF vs Flatpak, the Slant community recommends DNF for most people. In the question“What are the best Linux package managers?”DNF is ranked 6th while Flatpak is ranked 13th. The most important reason people chose DNF is:

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Pros

Pro

Delta RPMs

Pro

Fast dependency resolution

DNF uses a SAT solver for dependency resolution. This brings even more speed and avoids dependency hell.

Pro

Download multiple packages simultaneously for faster downloads

DNF can download packages concurrently for faster downloads.

Pro

Flexible runtime management

You can install a lot of runtimes for different apps, making applications a lot more compatible while still allowing some applications to share their runtimes.

Pro

A well-written documentation

Pro

Application sandboxing

All applications are limited to a set of predefined permissions, enhancing privacy and security.

Pro

Cross-distribution

You can install flatpak packages on any distro you want.

Cons

Con

Not yet at feature parity with YUM

As DNF is the successor to YUM, it still has a lot of features that are in YUM but that are missing here. Things like skipping broken package during install, debug, verbose output, enable repo or exclude packages during install have little to no support in DNF.